title: BIMLR: a method for constructing rooted phylogenetic networks from rooted phylogenetic trees.
abstract: Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The CASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved CASS algorithm, BIMLR. We show that BIMLR is faster than CASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/.
authors.affiliation: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, PR China. wangjuanangle@hit.edu.cn
authors.forename: Juan
authors.initials: J
authors.lastname: Wang
authors.forename: Maozu
authors.initials: M
authors.lastname: Guo
authors.forename: Linlin
authors.initials: L
authors.lastname: Xing
authors.forename: Kai
authors.initials: K
authors.lastname: Che
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Liu
authors.forename: Chunyu
authors.initials: C
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D008957:Models, Genetic; D010802:Phylogeny; D028201:Pinaceae / Q000235:genetics; D012984:Software
keywords: Evolution; Molecular evolution; Phylogenetic; e.g.; exempli gratia; i.e.; id est; w.r.t; with regard to